{"id":"https://openalex.org/W2951189966","doi":"https://doi.org/10.1186/s12859-018-2436-3","title":"ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events","display_name":"ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events","publication_year":2018,"publication_date":"2018-11-20","ids":{"openalex":"https://openalex.org/W2951189966","doi":"https://doi.org/10.1186/s12859-018-2436-3","mag":"2951189966","pmid":"https://pubmed.ncbi.nlm.nih.gov/30458725"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2436-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2436-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2436-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2436-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030595155","display_name":"Luca Denti","orcid":"https://orcid.org/0000-0001-8786-2276"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Luca Denti","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086249420","display_name":"Raffaella Rizzi","orcid":"https://orcid.org/0000-0001-9730-7516"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Raffaella Rizzi","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080398207","display_name":"Stefano Beretta","orcid":"https://orcid.org/0000-0003-4375-004X"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]},{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Beretta","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","Institute for Biomedical Technologies, National Council of Research, Segrate, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]},{"raw_affiliation_string":"Institute for Biomedical Technologies, National Council of Research, Segrate, Italy","institution_ids":["https://openalex.org/I4210154278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059679442","display_name":"Gianluca Della Vedova","orcid":"https://orcid.org/0000-0001-5584-3089"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gianluca Della Vedova","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103118099","display_name":"Marco Previtali","orcid":"https://orcid.org/0000-0003-3040-9539"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Previtali","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5038691764","display_name":"Paola Bonizzoni","orcid":"https://orcid.org/0000-0001-7289-4988"},"institutions":[{"id":"https://openalex.org/I66752286","display_name":"University of Milano-Bicocca","ror":"https://ror.org/01ynf4891","country_code":"IT","type":"education","lineage":["https://openalex.org/I66752286"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paola Bonizzoni","raw_affiliation_strings":["Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy. bonizzoni@disco.unimib.it","Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy. bonizzoni@disco.unimib.it","institution_ids":[]},{"raw_affiliation_string":"Department of Informatics, Systems, and Communication, University of Milano - Bicocca, Milan, Italy","institution_ids":["https://openalex.org/I66752286"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5030595155"],"corresponding_institution_ids":["https://openalex.org/I66752286"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.6755,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.84903098,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"19","issue":"1","first_page":"444","last_page":"444"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.6976521015167236},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.6127997040748596},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.5862787961959839},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5810785889625549},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5428280234336853},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46122390031814575},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.4553951621055603},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44867372512817383},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43491876125335693},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39337387681007385},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.38345685601234436},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.29849475622177124},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.24771273136138916},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.17387208342552185},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1441074013710022}],"concepts":[{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.6976521015167236},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.6127997040748596},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.5862787961959839},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5810785889625549},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5428280234336853},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46122390031814575},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.4553951621055603},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44867372512817383},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43491876125335693},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39337387681007385},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.38345685601234436},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.29849475622177124},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.24771273136138916},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.17387208342552185},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1441074013710022}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2436-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2436-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2436-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30458725","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30458725","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:boa.unimib.it:10281/215078","is_oa":false,"landing_page_url":"http://hdl.handle.net/10281/215078","pdf_url":null,"source":{"id":"https://openalex.org/S4306401259","display_name":"BOA (University of Milano-Bicocca)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:f5f7ce07af244d69bb57e0c34828675f","is_oa":true,"landing_page_url":"https://doaj.org/article/f5f7ce07af244d69bb57e0c34828675f","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-21 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5219951","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6247705","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2436-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2436-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2436-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5306454764","display_name":null,"funder_award_id":"2013--0955","funder_id":"https://openalex.org/F4320321499","funder_display_name":"Fondazione Cariplo"},{"id":"https://openalex.org/G8411802876","display_name":null,"funder_award_id":"2013-0955","funder_id":"https://openalex.org/F4320321499","funder_display_name":"Fondazione Cariplo"}],"funders":[{"id":"https://openalex.org/F4320321499","display_name":"Fondazione Cariplo","ror":"https://ror.org/01gb56c55"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2951189966.pdf","grobid_xml":"https://content.openalex.org/works/W2951189966.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1120389949","https://openalex.org/W1573352354","https://openalex.org/W1598909951","https://openalex.org/W1781218127","https://openalex.org/W1815037699","https://openalex.org/W1966822396","https://openalex.org/W2000875411","https://openalex.org/W2009329319","https://openalex.org/W2012660994","https://openalex.org/W2025119259","https://openalex.org/W2036897871","https://openalex.org/W2053057991","https://openalex.org/W2054576015","https://openalex.org/W2054895735","https://openalex.org/W2066231767","https://openalex.org/W2096465161","https://openalex.org/W2098832713","https://openalex.org/W2126419817","https://openalex.org/W2126766730","https://openalex.org/W2141458291","https://openalex.org/W2143447881","https://openalex.org/W2146487747","https://openalex.org/W2157560322","https://openalex.org/W2163516449","https://openalex.org/W2169456326","https://openalex.org/W2169603381","https://openalex.org/W2255131131","https://openalex.org/W2267092331","https://openalex.org/W2487999951","https://openalex.org/W2496794807","https://openalex.org/W2592811885","https://openalex.org/W2609675155","https://openalex.org/W2774883395","https://openalex.org/W2776539412","https://openalex.org/W2912383825","https://openalex.org/W2949317881","https://openalex.org/W2963037296","https://openalex.org/W2994805414","https://openalex.org/W6635755785"],"related_works":["https://openalex.org/W2321791250","https://openalex.org/W4213427798","https://openalex.org/W2023199111","https://openalex.org/W2564462691","https://openalex.org/W2065030615","https://openalex.org/W2885403345","https://openalex.org/W2052498125","https://openalex.org/W4387768639","https://openalex.org/W2094867951","https://openalex.org/W1535548930"],"abstract_inverted_index":{"Source":[0],"code,":[1],"documentation,":[2],"and":[3],"data":[4],"are":[5],"available":[6],"for":[7],"download":[8],"at":[9],"http://asgal.algolab.eu":[10],".":[11]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
